Variant report

Variant	rs57720404
Chromosome Location	chr9:95519404-95519405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95517729..95519725-chr9:95522515..95524617,2	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1010823	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821000	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821001	0.83[ASN][1000 genomes]
rs10821002	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821003	0.83[ASN][1000 genomes]
rs10821004	0.83[ASN][1000 genomes]
rs10821005	0.82[ASN][1000 genomes]
rs10821007	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821009	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821011	0.85[ASN][1000 genomes]
rs10821012	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821014	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10821015	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821016	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992402	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992403	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992404	0.80[EUR][1000 genomes]
rs10992406	0.80[EUR][1000 genomes]
rs10992413	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992414	0.81[ASN][1000 genomes]
rs10992416	0.83[ASN][1000 genomes]
rs10992417	0.83[ASN][1000 genomes]
rs10992418	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10992419	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992420	0.83[ASN][1000 genomes]
rs10992422	0.83[ASN][1000 genomes]
rs10992423	0.83[ASN][1000 genomes]
rs10992426	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992427	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992430	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992431	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992432	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992433	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992434	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992436	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992437	0.85[ASN][1000 genomes]
rs10992438	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992441	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992442	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992443	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992444	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992445	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992448	0.84[ASN][1000 genomes]
rs10992451	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992453	0.85[ASN][1000 genomes]
rs10992454	0.83[AFR][1000 genomes]
rs10992456	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992460	0.85[ASN][1000 genomes]
rs10992461	0.85[ASN][1000 genomes]
rs10992462	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992472	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1125063	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125064	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11533010	0.83[ASN][1000 genomes]
rs11535540	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12236393	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236516	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236747	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236754	0.85[ASN][1000 genomes]
rs12236788	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12237216	0.80[EUR][1000 genomes]
rs12238691	0.84[ASN][1000 genomes]
rs12683839	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12683944	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12684587	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12685080	0.89[ASN][1000 genomes]
rs12685256	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685358	0.83[ASN][1000 genomes]
rs12685780	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685791	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12686058	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1407944	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552908	0.90[AMR][1000 genomes]
rs1874128	0.86[AMR][1000 genomes]
rs1980705	0.85[AMR][1000 genomes]
rs2038686	0.86[AMR][1000 genomes]
rs2181584	0.83[ASN][1000 genomes]
rs2181586	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274413	0.86[AMR][1000 genomes]
rs2277164	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277166	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2281888	0.85[AMR][1000 genomes]
rs2296080	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3203916	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3739605	0.82[ASN][1000 genomes]
rs41266683	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4545157	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56111209	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56203846	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56311406	0.85[ASN][1000 genomes]
rs56339669	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57421019	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57737182	0.85[ASN][1000 genomes]
rs58045868	0.83[AMR][1000 genomes]
rs58952648	0.82[ASN][1000 genomes]
rs60173654	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60457563	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60498616	0.84[ASN][1000 genomes]
rs66493272	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68022962	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68046436	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031163	0.85[ASN][1000 genomes]
rs7037961	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753802	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753803	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753804	0.85[ASN][1000 genomes]
rs7850871	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7851947	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7860628	0.83[ASN][1000 genomes]
rs7862106	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7863890	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7864889	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7869529	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7869603	0.84[ASN][1000 genomes]
rs7875227	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8181065	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878610	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879812	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs912259	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912261	0.80[EUR][1000 genomes]
rs976320	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976321	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775970	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57720404	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95503800-95523800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:95509800-95522000	Weak transcription	Liver	Liver
3	chr9:95512000-95523400	Weak transcription	Aorta	Aorta
4	chr9:95512000-95525000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:95512200-95521800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:95512400-95521600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:95512400-95521600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:95512400-95522200	Weak transcription	NHDF-Ad	bronchial
9	chr9:95512400-95525200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:95512600-95521600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:95512600-95521800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:95512600-95525400	Weak transcription	A549	lung
13	chr9:95512800-95522200	Weak transcription	HSMM	muscle
14	chr9:95513000-95520000	Weak transcription	Brain Anterior Caudate	brain
15	chr9:95513000-95521800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:95513000-95522200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:95513000-95522400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:95513000-95522600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:95513600-95521600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:95513600-95521600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:95515000-95521600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:95515400-95521400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr9:95515400-95521800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:95515400-95521800	Weak transcription	Adipose Nuclei	Adipose
25	chr9:95515600-95521400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr9:95515600-95521600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr9:95515600-95521600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:95515600-95521800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:95515600-95522000	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:95515600-95523600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr9:95515600-95524800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:95517800-95520400	Enhancers	H1 Cell Line	embryonic stem cell
33	chr9:95518000-95519600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr9:95518200-95519600	Enhancers	Left Ventricle	heart
35	chr9:95518200-95522200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:95518200-95522400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:95518200-95523400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:95518400-95519600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:95518400-95519600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr9:95518400-95519600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:95518400-95519600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr9:95518400-95519600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr9:95518400-95521400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr9:95518400-95521600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:95518400-95521600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr9:95518400-95521600	Weak transcription	Brain Angular Gyrus	brain
47	chr9:95518400-95521600	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:95518400-95521600	Weak transcription	Right Ventricle	heart
49	chr9:95518400-95521800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr9:95518400-95521800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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